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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 2aa946176da7f19cb97e8903bbeded3e
+config: a117ea64eecff4bc3ebd3a3ca75869f9
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/index.html b/_modules/index.html
@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
-        <title>Overview: module code - MultiAssayExperiment 0.4.0 documentation</title>
+        <title>Overview: module code - MultiAssayExperiment 0.4.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MultiAssayExperiment 0.4.0 documentation</div></a>
+      <a href="../index.html"><div class="brand">MultiAssayExperiment 0.4.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.0 documentation</span>
+  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.1 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -241,7 +241,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=6c02275b"></script>
+</div><script src="../_static/documentation_options.js?v=c87aa342"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/multiassayexperiment/MultiAssayExperiment.html b/_modules/multiassayexperiment/MultiAssayExperiment.html
diff --git a/_modules/multiassayexperiment/io/h5ad.html b/_modules/multiassayexperiment/io/h5ad.html
@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../../genindex.html" /><link rel="search" title="Search" href="../../../search.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
-        <title>multiassayexperiment.io.h5ad - MultiAssayExperiment 0.4.0 documentation</title>
+        <title>multiassayexperiment.io.h5ad - MultiAssayExperiment 0.4.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">MultiAssayExperiment 0.4.0 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">MultiAssayExperiment 0.4.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.0 documentation</span>
+  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.1 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -264,7 +264,7 @@ <h1>Source code for multiassayexperiment.io.h5ad</h1><div class="highlight"><pre
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=6c02275b"></script>
+</div><script src="../../../_static/documentation_options.js?v=c87aa342"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_modules/multiassayexperiment/io/interface.html b/_modules/multiassayexperiment/io/interface.html
@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../../genindex.html" /><link rel="search" title="Search" href="../../../search.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
-        <title>multiassayexperiment.io.interface - MultiAssayExperiment 0.4.0 documentation</title>
+        <title>multiassayexperiment.io.interface - MultiAssayExperiment 0.4.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -122,7 +122,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">MultiAssayExperiment 0.4.0 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">MultiAssayExperiment 0.4.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -145,7 +145,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.0 documentation</span>
+  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.1 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -313,7 +313,7 @@ <h1>Source code for multiassayexperiment.io.interface</h1><div class="highlight"
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=6c02275b"></script>
+</div><script src="../../../_static/documentation_options.js?v=c87aa342"></script>
     <script src="../../../_static/doctools.js?v=888ff710"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/_sources/changelog.md.txt b/_sources/changelog.md.txt
@@ -1,6 +1,18 @@
 # Changelog
 
-## Version 0.3.0 (development)
+## Version 0.4.0
+
+This is a complete rewrite of the package, following the functional paradigm from our [developer notes](https://github.com/BiocPy/developer_guide#use-functional-discipline).
+
+- `column_data` and `sample_map` are expected to be `BiocFrame` objects and will be converted if a pandas `DataFrame` is provided. This will allows us to reduce complexity and provide consistent downstream operations.
+- A `sample_map` will be created by default if both `column_data` and `sample_map` are None.
+- A warning is raised if `column_names` are empty for an experiment.
+- A warning is raised if `column_data` contains duplicate row names.
+- Streamlines subset operation.
+- Reduce dependency on a number of external packages.
+- Update docstrings, tests and docs.
+
+## Version 0.3.0
 
 This release migrates the package to a more palatable Google's Python style guide. A major modification to the package is with casing, all `camelCase` methods, functions and parameters are now `snake_case`.
 

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.4.0',
+    VERSION: '0.4.1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/api/modules.html b/api/modules.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="multiassayexperiment package" href="multiassayexperiment.html" /><link rel="prev" title="Tutorial" href="../tutorial.html" />
 
     <!-- Generated with Sphinx 7.2.6 and Furo 2023.09.10 -->
-        <title>multiassayexperiment - MultiAssayExperiment 0.4.0 documentation</title>
+        <title>multiassayexperiment - MultiAssayExperiment 0.4.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?v=36a5483c" />
@@ -123,7 +123,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">MultiAssayExperiment 0.4.0 documentation</div></a>
+      <a href="../index.html"><div class="brand">MultiAssayExperiment 0.4.1 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.0 documentation</span>
+  <span class="sidebar-brand-text">MultiAssayExperiment 0.4.1 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -243,6 +243,7 @@ <h1>multiassayexperiment<a class="headerlink" href="#multiassayexperiment" title
 <li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_experiments"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.get_experiments()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_metadata"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.get_metadata()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_sample_map"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.get_sample_map()</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.get_with_column_data"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.get_with_column_data()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.metadata"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.metadata</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.replicated"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.replicated()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="multiassayexperiment.html#multiassayexperiment.MultiAssayExperiment.MultiAssayExperiment.sample_map"><code class="docutils literal notranslate"><span class="pre">MultiAssayExperiment.sample_map</span></code></a></li>
@@ -326,7 +327,7 @@ <h1>multiassayexperiment<a class="headerlink" href="#multiassayexperiment" title
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=6c02275b"></script>
+</div><script src="../_static/documentation_options.js?v=c87aa342"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=32e29ea5"></script>